appendix_a
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+ | ====== PolyPhen-2 annotation summary report explained ====== | ||
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+ | Following is a description of **PolyPhen-2** annotation summary report. Reports in this format are produced by both PolyPhen-2 **Batch query** web service, as well as by **standalone** PolyPhen-2 software. It is a plain text tab-separated file with each line annotating single protein variant (amino acid residue substitution). | ||
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+ | Eleven columns highlighted below (1, 5-9, 12, 16-18, 56) are the ones included in the **Short** version of the report available via **Batch query** web page. These are sufficient if you are interested in PolyPhen-2 prediction outcome and prediction confidence scores. The rest of the columns in **Full** report version are mostly useful only if you want to investigate all features supporting the prediction in detail. | ||
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+ | ^ Column\\ No. ^ Column\\ Name ^ Description | ||
+ | | **Original query** (as copied from user input): | ||
+ | ^ 1 | o_acc | original protein identifier | | ||
+ | | 2 | o_pos | original substitution position in the protein sequence | | ||
+ | | 3 | o_aa1 | original wild type (reference) amino acid residue | | ||
+ | | 4 | o_aa2 | original mutant (substitution) amino acid residue | | ||
+ | | **Annotated query**: | ||
+ | ^ 5 | rsid | dbSNP reference SNP identifier (rsID) if available | | ||
+ | ^ 6 | acc | UniProtKB accession if known protein, otherwise same as o_acc | | ||
+ | ^ 7 | pos | substitution position in UniProtKB protein sequence, otherwise same as o_pos | | ||
+ | ^ 8 | aa1 | wild type amino acid residue in relation to UniProtKB sequence | ||
+ | ^ 9 | aa2 | mutant amino acid residue in relation to UniProtKB sequence | | ||
+ | | 10 | nt1 | wild type (reference) allele nucleotide | | ||
+ | | 11 | nt2 | mutant allele nucleotide | | ||
+ | | **PolyPhen-2 prediction outcome**: | ||
+ | ^ 12 | prediction | ||
+ | | **PolyPhen-1 prediction description** (obsolete, please ignore): | ||
+ | | 13 | based_on | ||
+ | | 14 | effect | ||
+ | | **PolyPhen-2 classifier outcome and scores**: | ||
+ | | 15 | pph2_class | ||
+ | ^ 16 | pph2_prob | ||
+ | ^ 17 | pph2_FPR | ||
+ | ^ 18 | pph2_TPR | ||
+ | | 19 | pph2_FDR | ||
+ | | **UniProtKB/ | ||
+ | | 20 | site | substitution SITE annotation | | ||
+ | | 21 | region | ||
+ | | 22 | PHAT | PHAT matrix element for substitutions in the TRANSMEM region | | ||
+ | | **Multiple sequence alignment scores**: | ||
+ | | 23 | dScore | ||
+ | | 24 | Score1 | ||
+ | | 25 | Score2 | ||
+ | | 26 | MSAv | version of the multiple sequence alignment used in conservation scores calculations: | ||
+ | | 27 | Nobs | number of residues observed at the substitution position in multiple alignment (without gaps) | | ||
+ | | **Protein 3D structure features**: | ||
+ | | 28 | Nstruct | ||
+ | | 29 | Nfilt | number of 3D BLAST hits after identity threshold filtering | | ||
+ | | 30 | PDB_id | ||
+ | | 31 | PDB_ch | ||
+ | | 32 | length | ||
+ | | 33 | PDB_pos | ||
+ | | 34 | ident | sequence identity between query sequence and aligned PDB sequence | | ||
+ | | 35 | dVol | change in residue side chain volume | | ||
+ | | 36 | dProp | change in solvent accessible surface propensity resulting from the substitution | | ||
+ | | 37 | SecStr | ||
+ | | 38 | MapReg | ||
+ | | 39 | NormASA | ||
+ | | 40 | B-fact | ||
+ | | 41 | H-bonds | ||
+ | | 42 | AveNHet | ||
+ | | 43 | MinDHet | ||
+ | | 44 | AveNInt | ||
+ | | 45 | MinDInt | ||
+ | | 46 | AveNSit | ||
+ | | 47 | MinDSit | ||
+ | | **Nucleotide sequence context features**: | ||
+ | | 48 | Transv | ||
+ | | 49 | CodPos | ||
+ | | 50 | CpG | whether substitution changes CpG context: 0\ -\ non-CpG context retained, 1\ -\ removes CpG site, 2\ -\ creates new CpG site, 3\ -\ CpG context retained | | ||
+ | | 51 | MinDJnc | ||
+ | | **Pfam protein family**: | ||
+ | | 52 | PfamHit | ||
+ | | **Substitution scores**: | ||
+ | | 53 | IdPmax | ||
+ | | 54 | IdPSNP | ||
+ | | 55 | IdQmin | ||
+ | | **Comments**: | ||
+ | ^ 56 | Comments | ||
appendix_a.txt · Last modified: 2021/12/03 23:06 by 127.0.0.1